REDCAT-lab-2010-rev

REDCAT-lab-2010-rev - REDCAT LABORATORY EXERCISE BCMB/CHEM...

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REDCAT LABORATORY EXERCISE BCMB/CHEM 8190, April 9, 2010 Installation note for instructors: REDCAT may be downloaded from: http://ifestos.cse.sc.edu/software.php#redcat You will also find further instructions and a manual accessible on the pages that appear. Versions exist for Linux and Mac OS X. REDCAT uses gnuplot and Tcl/Tk 8.0 or later. Input files may be obtained from: http://tesla.ccrc.uga.edu/courses/bionmr/labs/ The tarball (redcat-lab-2010.tar) includes: REDCAT-lab-2010.pdf (this file) 1bq8.pdb, 1bq8-frag1-1-25.pdb, 1bq8-frag2-27-54.pdb (the protein structure files) 1bq8-RDCs-2-53.txt, 1bq8-RDCs-27-53.txt (the residual dipolar coupling files) map.dat, map3D.dat (files used in plotting results in REDCAT) Laboratory exercise: Introduction. REDCAT (REsidual Dipolar Coupling Analysis Tool), is a program that aids the interpretation of residual dipolar couplings (RDCs) in terms of structural models. It is primarily designed to test RDC data for consistency with structural models, but it can also aid in the assembly of structures from fragments by orienting each fragment in a common principal alignment frame. It incorporates a number of other useful tools such as graphical display of principal axis directions and prediction of averaging effects on RDCs for comparison with experimental data. It operates by taking in coordinates for various dipole interaction vectors (H-N bonds for example) and experimental RDCs, and then solving for an order tensor by singular value decomposition. It does this thousands of times using a random sampling of RDCs within defined error limits to produce a picture of reliability of results. REDCAT has been installed on the computers you are using (or is accessible by opening a remote shell for a server having REDCAT installed). The instructions that follow are intended to supplement the manual by leading you through an exercise that manipulates data on a small paramagnetic protein, rubredoxin. The RDCs are only for H-N vectors. They are small in magnitude because they were collected using only natural field induced orientation of this paramagnetic protein. However, the data should suffice to illustrate principles of the program. You will first use data for the intact protein, and use REDCAT tools to evaluate consistency between RDC data and a crystal structure. You will then do a fragment assembly project in which the protein has been divided into two parts with one rotated from its original orientation. You will use REDCAT tools to reestablish the proper orientation.
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Step 1. Creating an input file
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REDCAT-lab-2010-rev - REDCAT LABORATORY EXERCISE BCMB/CHEM...

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